Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists

2016 ◽  
Vol 94 ◽  
pp. 718-729 ◽  
Author(s):  
Yan Zhao ◽  
Zhenzhen Yi ◽  
Eleni Gentekaki ◽  
Aibin Zhan ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Species Identification ◽  
Morphological Characters ◽  
Mitochondrial Genes

scholarly journals Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Shen ◽  
Shi-Liang Liu ◽  
Ji-Hang Jiang ◽  
Li-Wei Zhou
Keyword(s):  
Species Identification ◽  
Rolling Circle Amplification ◽  
Practical Method ◽  
Morphological Characters ◽  
Its Sequences ◽  
Commercial Development ◽  
Medicinal Mushrooms ◽  
Rolling Circle ◽  
Reference Sequences ◽  
Its Barcoding

Abstract“Sanghuang” refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of “Sanghuang” in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to “Sanghuang” in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.

scholarly journals Nothing in (sponge) biology makes sense – except when based on holotypes

2015 ◽  
Vol 96 (2) ◽  
pp. 305-311 ◽  
Author(s):  
Dirk Erpenbeck ◽  
Merrick Ekins ◽  
Nicole Enghuber ◽  
John N.A. Hooper ◽  
Helmut Lehnert ◽  
...  
Keyword(s):  
New Species ◽  
Reference Material ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Reference Sequences ◽  
Species Descriptions ◽  
Preservation History

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.

scholarly journals Pupae of the Nearctic species of Culicoides Latreille subgenus Monoculicoides Khalaf (Diptera: Ceratopogonidae)

Zootaxa ◽  
2018 ◽  
Vol 4504 (4) ◽  
pp. 451
Author(s):  
PHILLIP SHULTS ◽  
ART BORKENT
Keyword(s):  
Species Identification ◽  
Morphological Characters ◽  
Valid Species ◽  
Biogeographic Region ◽  
Nearctic Region

There are 160 valid species of Culicoides Latreille described from the Nearctic Region, but many are unknown as immatures or, although partially described, cannot be readily identified. We provide pupal diagnoses, descriptions, and a key to all seven known species of Culicoides subgenus Monoculicoides Khalaf occurring in the Nearctic biogeographic region. A diagnosis of several characters unique to this subgenus is provided to allow for the recognition of the included species from those of other subgeneric groupings. Microphotography of important morphological characters for both the key and descriptions are provided. This study highlights the usefulness of examining the pupae of Culicoides as a tool for species identification. The pupae of Culicoides grandensis Grogan & Phillips, C. occidentalis Wirth & Jones, and C. shemanchuki Grogan & Lysyk are newly described and those of C. riethi Kieffer, C. stigma (Meigen), and C. variipennis Wirth & Jones are redescribed in detail. The seventh species, C. sonorensis, was fully described recently. 

Systematics and phylogeography of the Australasian mangrove crabs Parasesarma semperi and P. longicristatum (Decapoda : Brachyura : Sesarmidae) based on morphological and molecular data

2018 ◽  
Vol 32 (1) ◽  
pp. 196 ◽  
Author(s):  
Adnan Shahdadi ◽  
Peter J. F. Davie ◽  
Christoph D. Schubart
Keyword(s):  
Genetic Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Geographic Range ◽  
The Philippines ◽  
Mitochondrial Genes ◽  
Width Ratio ◽  
Sister Relationship ◽  
Mangrove Crabs ◽  
Morphological And Molecular Data

Parasesarma semperi (Bürger, 1893) was first described from Bohol in the Philippines and is considered to be widely distributed in Southeast Asia. Parasesarma longicristatum (Campbell, 1967) was originally described as a subspecies of P. semperi from Queensland, Australia, and later recognised as a full species. In this study, we re-examine specimens of the two species from across their entire geographic range using genetic markers, a morphometric analysis, and traditional morphological characters. Previous taxonomic species diagnoses were found to be unreliable, but morphometric principle component analyses consistently separate the two species, with the length to width ratio of the propodus of the fourth pereiopod being of particular importance. Genetic data corresponding to the mitochondrial genes COI, ND1 and 16S confirmed a close sister relationship between the two species, forming reciprocally monophyletic groups. Both species have high haplotype diversities and high intraspecific gene flow.

Male identification, generic classification and sexual dimorphism of Micronychus pardus (Kazantsev, 2018) comb. nov. (Coleoptera: Lycidae: Calochrominae)

Zootaxa ◽  
2019 ◽  
Vol 4657 (1) ◽  
pp. 177-182 ◽  
Author(s):  
MICHAL MOTYKA
Keyword(s):  
Mitochondrial Dna ◽  
Sexual Dimorphism ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Large Specimen ◽  
Molecular Analyses ◽  
Almost All ◽  
First Time

Almost all net-winged beetles are members of Müllerian complexes and their similarity due to phenotypic coevolution sometimes complicates species identification and generic placement. Therefore, large specimen series, detailed exhaustive examination of morphological characters and molecular data are needed to clarify the taxonomic placement. Using mitochondrial DNA sequences, I investigated the sexual dimorphism and generic placement of the recently described species Calochromus pardus Kazantsev, 2018. I found that the species does not belong in Calochromus Guérin-Méneville, 1833 and all morphological characters and molecular analyses point to its placement in Micronychus Motschulsky, 1861. Therefore, Micronychus pardus (Kazantsev, 2018), comb. nov. is proposed. Additionally, the male is described here for the first time showing the sexual dimorphism in the species. Unlike the females, the males do not superficially resemble members of Xylobanus Waterhouse, 1879 with bright coloured elytral costae and black background, but mimics the sympatrically occurring yellow and black lycids in the genus Cautires Waterhouse, 1879. 

scholarly journals Identification key to the Anopheles mosquitoes of South America (Diptera: Culicidae). III. Male genitalia

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Maria Anice Mureb Sallum ◽  
Ranulfo González Obando ◽  
Nancy Carrejo ◽  
Richard C. Wilkerson
Keyword(s):  
South America ◽  
Species Identification ◽  
Male Genitalia ◽  
Morphological Characters ◽  
Identification Key ◽  
Careful Examination ◽  
South American ◽  
Type Specimens ◽  
South American Species ◽  
Accurate Identification

Abstract Background Accurate identification of the species of Anopheles Meigen, 1818 requires careful examination of all life stages. However, morphological characters, especially those of the females and fourth-instar larvae, show some degree of polymorphism and overlap among members of species complexes, and sometimes even within progenies. Characters of the male genitalia are structural and allow accurate identification of the majority of species, excluding only those in the Albitarsis Complex. In this key, based on the morphology of the male genitalia, traditionally used important characters are exploited together with additional characters that allow robust identification of male Anopheles mosquitoes in South America. Methods Morphological characters of the male genitalia of South American species of the genus Anopheles were examined and employed to construct a comprehensive, illustrated identification key. For those species for which specimens were not available, illustrations were based on published illustrations. Photographs of key characters of the genitalia were obtained using a digital Canon Eos T3i attached to a light Diaplan Leitz microscope. The program Helicon Focus was used to build single in-focus images by stacking multiple images of the same structure. Results An illustrated key to South American species of Anopheles based on the morphology of the male genitalia is presented, together with a glossary of morphological terms. The male genitalia of type-specimens of previously poorly documented species were also examined and included in the key, e.g. Anopheles (Anopheles) tibiamaculatus (Neiva, 1906) which has a unique quadrangular-shaped aedeagus with an apical opening. Conclusions Male genitalia of South American species of Anopheles possess robust characters that can be exploited for accurate species identification. Distortion that can occur during the dissection and mounting process can obstruct accurate identification; this is most evident with inadvertent damage or destruction of unique features and interferes with correctly assigning shapes of the features of the ventral claspette. In some species, the shape, and anatomical details of the aedeagus also need to be examined for species identification. For members of the Myzorhynchella Series, both ventral and dorsal claspettes possess multiple characteristics that are herein used as reliable characters for species identification.

scholarly journals Foliar trichomes of Croton L. (Euphorbiaceae: Crotonoideae) from China and its taxonomic implications

2013 ◽  
Vol 20 (1) ◽  
pp. 85-94 ◽  
Author(s):  
Huan-Fang Liu ◽  
Yun-Fei Deng ◽  
Jing-Ping Liao
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Species Identification ◽  
Morphological Characters ◽  
Plant Taxon ◽  
Taxonomic Implications ◽  
Sectional Classification ◽  
Trichome Types ◽  
Trichome Morphology ◽  
Scanning Electron

Foliar trichomes of 21 species of the genus Croton L. from China have been examined using stereomicroscopy and scanning electron microscopy. Five trichome types characterized by their morphology are identified, viz., stellate, lepidote, simple, dendritic and appressed-rosulate. Only stellate trichome is observed in most species, with only six species that are found to maintain two or three trichome types. Trichome types and density are useful for species identification and sectional classification for Chinese species. Based on the trichome types and other morphological characters, 21 Chinese species are proposed to be placed in five sections. Croton crassifolius belongs to sect. Andrichnia; C. cascarilloides belongs to sect. Monguia; C. mangelong, C. kongensis, C. laevigatus and C. laniflorus belong to sect. Argyrocroton; C. lauioides, C. howii and C. damayeshu belong to sect. Adenophylli. The remaining Chinese Croton species might be placed into sect. Croton. A key for Chinese Croton species based on trichome morphology is provided.DOI: http://dx.doi.org/10.3329/bjpt.v20i1.15468Bangladesh J. Plant Taxon. 20(1): 85-94, 2013 (June)

scholarly journals The Utility of DNA Barcoding for the Species Identification of Larval Fish in the Lower Ing River, Thailand

2020 ◽  
Vol 20 (9) ◽  
pp. 671-679
Author(s):  
Dutrudi Panprommin ◽  
Kanyanat Soontornprasit ◽  
Siriluck Tuncharoen ◽  
Niti Iamchuen
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Larval Fish ◽  
Average Length ◽  
Conservation Status ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Coi Gene ◽  
Fishery Resource ◽  
Sustainable Fishery

The species identification of larval fish is very important for sustainable fishery resource management. However, identification based on morphological characters is very difficult, complex and error-prone. DNA barcoding with the sequence of cytochrome c oxidase I (COI) gene was used to identify larval fish species from 10 stations in the tributaries of the lower Ing River. One hundred and six samples were collected between May 2016 and April 2017. The average length of the COI nucleotide sequences was approximately 640 bp. A total of 99 nucleotide sequences were identified in 35 species, 31 genera, 19 families and 9 orders, with 97-100% identity with entries in both the GenBank and BOLD databases. The genetic distance within species ranged from 0.000 to 0.004. However, seven samples were identified at only the genus level because their sequences had not been reported in any databases. Based on IUCN conservation status, most species were classified as least concern (77.14%). Approximately 69.23% of all species were related to human uses in fisheries, aquaculture or aquariums, whereas 30.77% of species were not assessed. Trichopsis vittata (family Osphronemidae) (90%) had the most frequency of occurrence, followed by Oryzias minutillus (family Adrianichthyidae) (70%) and Trichopodus trichopterus (family Osphronemidae) (70%).

scholarly journals *) Penulis Penanggung Jawab STUDI TAKSONOMI BINTANG LAUT (Asteroidea, Echinodermata) DARI KEPULAUAN KARIMUNJAWA, JEPARA

2012 ◽  
Vol 1 (1) ◽  
pp. 59-65
Author(s):  
Puspitasari
Keyword(s):  
Coral Reef ◽  
Food Webs ◽  
Species Identification ◽  
Morphological Characters ◽  
Sea Stars ◽  
Eastern Side ◽  
Northern Side ◽  
Western Side ◽  
Biology Laboratory ◽  
Linckia Laevigata

Bintang laut merupakan salah satu kelompok echinodermata yang berperan penting dalam jaring makanan, umumnya sebagai predator dan pemakan detritus. Penelitian ini dilaksanakan pada bulan Desember 2011 – Maret 2012. Penelitian ini bertujuan untuk mengetahui jenis, habitat dan ciri-ciri khusus bintang laut dari perairan Karimunjawa, Jepara. Pengambilan sampel dilakukan di kepulauan Karimunjawa, mencakup sisi barat dan timur pulau Karimunjawa, sisi barat pulau Menjangan Kecil, sisi utara pulau Cemara Kecil dan sisi utara pulau Cemara Besar, menggunakan metode purposive sampling. Sampel bintang laut dikumpulkan dari berbagai habitat di daerah intertidal sampai kedalaman 3 meter. Identifikasi setiap spesies dan pembuatan kunci identifikasi dilakukan di Pusat Penelitian Oseanografi (P2O-LIPI), Jakarta. Sebelas individu bintang laut dari 9 spesies yang mewakili 6 genera dari 4 famili dan 2 ordo berhasil di identifikasi. Sebagian besar bintang laut ditemukan di daerah terumbu karang. Berdasarkan karakter morfologi diketahui bahwa spesies yang tampaknya sama bahkan hidup di lokasi yang sama ternyata adalah spesies yang berbeda yaitu Archaster angulatus dan Archaster typicus, Nardoa frianti dan Nardoa pauciforis serta Linckia laevigata dan Linckia multifora. Semua jenis bintang laut yang dikumpulkan merupakan jenis-jenis yang umum ditemukan di perairan Indonesia.Kata Kunci : Taksonomi, Identifikasi, Bintang Laut, KarimunjawaAbstractSea stars play an important role in food webs, generally as predators and detritus feeder. This research has been conducted in December 2011 – March 2012. This research is subjected to achieved its biodiversity in the Karimunjawa Islands. Samples were collected from western and eastern side of Karimunjawa Island, western side of Menjangan Kecil, northern side of Cemara Kecil and northern side of Cemara Besar island, up to the depth of three meters. Species identification was done at Biology Laboratory of the Research Center for Oceanography (P2O-LIPI) Jakarta. A total of 11 asteroid individuals belonging to 9 species of 6 genera, which represented 4 families and 2 orders have been identified. Most of sea stars were found on the coral reef. Based on morphological characters of sea stars that apparently similar, even living in the same location, however after identified are different species, that is Archaster angulatus and Archaster typicus, Nardoa frianti and Nardoa pauciforis then Linckia laevigata and Linckia multifora. All species was considered common for tropical Indo Pasific region, including Indonesian watersKeywords: Taxonomical, Identification, Asteroidea, Karimunjawa

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